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The EcoSim was updated to use the vertical semi-Lagrangian sinking flux for fecal material available in ROMS. This generic sinking is identical to that found in other ROMS ecosystem and sediment models. It also includes a simple biological sedimentation (BIO_SEDIMENT option) which remineralizes particular nitrogen and returns it into the dissolved nitrate pool.

Many thanks to Bronwyn Cahill for implementing and testing these algorithms.

Oops, I loaded the wrong ad_set_depth.F file in ​src:ticket:285 from my private research branch. The changes due the update of the vertical coordinate system in ROMS will be release latter in the week.

The correction that I needed to load was due to stratigraphy. The codes were inconsistent. The good news is the changes due to SED_MORPH and SEDIMENT are not yet supported in the adjoint-based algorithms.

This is a major redo of ROMS vertical coordinates. It was expanded to support an additional transformation and numerous vertical stretching functions. The original transformation and vertical stretching function is still available.

All the input scripts (ocean*.in) were modified to include two new vertical coordinate parameters:

! Set vertical, terrain-following coordinates transformation equation and
! stretching function (see below for details), [1:Ngrids].

  Vtransform == 1                          ! transformation equation
 Vstretching == 1                          ! stretching function

There is extensive documentation about this in standard input script (ocean*.in) and ​WikiROMS. Also check the following message in the ​forum.

Many thanks to Sasha Shchepetkin for providing us his tranformation and vertical stretching function (available in UCLA-ROMS as default), Rocky Geyer for providing us a new vertical stretching function for sediment applications in shallow grids, Andy Moore for his help checking these transformations in the adjoint codes, and Rich Signell for his help with CF Conventions Committe and the NetCDF-Java Group.